期刊
THEORETICAL BIOLOGY AND MEDICAL MODELLING
卷 2, 期 -, 页码 -出版社
BMC
DOI: 10.1186/1742-4682-2-23
关键词
-
资金
- Deutsche Forschungsgemeinschaft (DFG) [Sonderforschungsbereich 386]
Background: The study of the network between transcription factors and their targets is important for understanding the complex regulatory mechanisms in a cell. Unfortunately, with standard microarray experiments it is not possible to measure the transcription factor activities (TFAs) directly, as their own transcription levels are subject to post-translational modifications. Results: Here we propose a statistical approach based on partial least squares (PLS) regression to infer the true TFAs from a combination of mRNA expression and DNA-protein binding measurements. This method is also statistically sound for small samples and allows the detection of functional interactions among the transcription factors via the notion of meta-transcription factors. In addition, it enables false positives to be identified in ChIP data and activation and suppression activities to be distinguished. Conclusion: The proposed method performs very well both for simulated data and for real expression and ChIP data from yeast and E. Coli experiments. It overcomes the limitations of previously used approaches to estimating TFAs. The estimated profiles may also serve as input for further studies, such as tests of periodicity or differential regulation. An R package plsgenomics implementing the proposed methods is available for download from the CRAN archive.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据